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title: Current Projects
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#Current Projects

###Ecological and Evolutionary processes in the long-term E. coli evolution experiment

Working with Jeff Barrick and Austin Meyer, I collected data on how allele frequencies change over time in the Ara-1 lineage of the long-term evolution experiment. These data are inconsistent with simple models of asexual evolution that have been fitted to these data. This led us to hypothesize that transient frequency-dependent interactions evolve on short time-scales, resulting in the observed deviation from theory. I confirmed the existence of these interactions, and pinned down their genetic basis. Currently, I am working with Noah Ribeck to develop more sophisticated models of evolution in the long-term experiment that take these eco-evolutionary dynamics into account.


	
###Comparative Genomics with the long-term evolution experiment

The long-term evolution experiment is a powerful model system both for dissecting evolutionary and ecological processes, and for testing theory. But how relevant is the experiment for understanding how microbial communities evolve in the real world? In terms of evolutionary change, the most obvious difference between dynamics in the experiment, versus the real world, is the lack of recombination, horizontal gene transfer, and of viruses that can act as vectors for strange genetic material.
I'm interested in comparing the dynamics of genome evolution between wild E. coli and the long-term experiment to explore these issues. In particular, my current work focuses on how multi-level selection shapes genome structure. My working hypothesis is that bacteria are porous organisms, akin to communities of genes that work together, often susceptible to cheating as well as cooperation on the gene level. This view of evolution as operating on multiple, recursive levels is deeply appealing to me, intellectually. I’m working on cashing out a few predictions of this model, such as 1) some genes should have larger effective population sizes than the organism they live in; 2) different genes might have different strategies for survival in a community; 3) many genes in bacterial genomes might not be adaptive—and might even be maladaptive as genetic parasites; 4) genomes and genetic elements in general might be intrinsically modular in terms of how cooperative their dynamics are; and 5) The network of genetic interactions between alleles should be structured by genes evolving to be resistant to replacement by alleles from the outside, while simultaneously trying to be able to replace alleles in other genetic backgrounds. 
I think this work has deep implications for our understanding of sex and speciation—but most of this work is provisional at the moment.


	
###Epistasis and Modularity  


I have helped Mike Wiser and Jeff Morris engineer parallel evolving alleles at the spoT locus in Esherichia coli among genetic backgrounds. We are interested in how tightly integrated these alleles are into the rest of the genome.

In my work with the Ara-1 lineage of the long-term experiment, I am testing whether an allele in nadR might be a niche-specific adaptive mutation. I am asking whether this allele is maladaptive if placed in the genome of a competing, frequency-dependent strain, due to competing demands on redox-balance. This question is inspired by Zachary Blount's larger research agenda on speciation and niche-specific adaptive mutations on citrate in the Ara-3 lineage of the long-term adaptive experiment. This work is an experimental complement to my research on genome structure in wild E. coli, compared to our domesticated lines.
